It will scan every file on your system with the exception of archives (if you didn't select them).
So by its name the thorough scan is very thorough and more so if you select archives.
You don't say a) anything about your system spec, CPU, RAM, etc. or b) how much data is in the hard disks that are being scanned, so there really is no way to say if it might extend to 240+ minutes.
I believe the VPS update goes on, it was suggested that you would still want the best/latest signatures by one of the Alwil team some time ago. But, I for a start wouldn't be going on-line whilst running a thorough scan in the first place. If you don't have an off switch on your modem/router then perhaps you could disable outbound connection in your firewall, many have this software switch/block all function.